Merge pull request #1575 from ComparativeGenomicsToolkit/oneshot

fix toil dependency bug in recent vcf refactor
ComparativeGenomicsToolkit · Dec 31, 2024 · 1665087 · 1665087
2 parents 0ecf101 + 64292d0
commit 1665087
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/src/cactus/refmap/cactus_graphmap_join.py b/src/cactus/refmap/cactus_graphmap_join.py
@@ -580,11 +580,13 @@ def graphmap_join_workflow(job, options, config, vg_ids, hal_ids):
 
         # optional vcf
         if workflow_phase in options.vcf:
-            vcf_prev_job = ref_fasta_job if ref_fasta_job else gfa_root_job
             for vcf_ref in options.vcfReference:
-                vcf_job = vcf_prev_job.addFollowOnJobFn(make_vcf, config, options, workflow_phase,
+                vcf_job = gfa_root_job.addFollowOnJobFn(make_vcf, config, options, workflow_phase,
                                                         index_mem, vcf_ref, phase_vg_ids,
                                                         ref_fasta_job.rv() if ref_fasta_job else None)
+                if ref_fasta_job:
+                    ref_fasta_job.addFollowOn(vcf_job)
+
                 out_dicts.append(vcf_job.rv())
 
         # optional giraffe